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- PDB-4oqu: Structure of the SAM-I/IV riboswitch (env87(deltaU92)) -

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Basic information

Entry
Database: PDB / ID: 4oqu
TitleStructure of the SAM-I/IV riboswitch (env87(deltaU92))
ComponentsSAM-I/IV riboswitch
KeywordsRNA / riboswitch / aptamer / pseudoknot / regulation / S-adenosylmethionine
Function / homologyS-ADENOSYLMETHIONINE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTrausch, J.J. / Reyes, F.E. / Edwards, A.L. / Batey, R.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for diversity in the SAM clan of riboswitches.
Authors: Trausch, J.J. / Xu, Z. / Edwards, A.L. / Reyes, F.E. / Ross, P.E. / Knight, R. / Batey, R.T.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-I/IV riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1427
Polymers31,6221
Non-polymers5206
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.269, 127.269, 181.609
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: RNA chain SAM-I/IV riboswitch


Mass: 31622.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: T7 transcription
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4- ...Details: 1:1 mix of RNA mix and mother liquor. RNA mix contained RNA and 1 mM SAM. Mother liquor contained 50 mM Na-cacodylate, pH 7.0, 250 mM ammonium acetate, 20 mM MgCl2, and 16% 2-methyl-2,4-pentanediol (MPD), VAPOR DIFFUSION, HANGING DROP, temperature 303.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 17, 2014
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.2→41.66 Å / Num. all: 14952 / Num. obs: 14916 / % possible obs: 99.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→31.408 Å / SU ML: 0.41 / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1486 10 %10%
Rwork0.1957 ---
obs0.1987 14854 99.42 %-
all-14854 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→31.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2100 32 0 2132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062383
X-RAY DIFFRACTIONf_angle_d1.2523718
X-RAY DIFFRACTIONf_dihedral_angle_d12.8841162
X-RAY DIFFRACTIONf_chiral_restr0.052491
X-RAY DIFFRACTIONf_plane_restr0.00799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.30320.39821320.35471183X-RAY DIFFRACTION100
3.3032-3.42110.32271290.31781186X-RAY DIFFRACTION99
3.4211-3.55790.30011330.29631194X-RAY DIFFRACTION99
3.5579-3.71960.28441320.24641175X-RAY DIFFRACTION99
3.7196-3.91540.27291330.22781198X-RAY DIFFRACTION100
3.9154-4.16020.22421330.2141195X-RAY DIFFRACTION100
4.1602-4.48050.23181350.19831210X-RAY DIFFRACTION100
4.4805-4.92990.24611350.16461225X-RAY DIFFRACTION100
4.9299-5.63970.1731370.14851223X-RAY DIFFRACTION100
5.6397-7.09190.18881400.16541260X-RAY DIFFRACTION100
7.0919-31.40930.20891470.1821319X-RAY DIFFRACTION98

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